Add metrics endpoint

datameta/api/__init__.py

@@ -12,15 +12,15 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from pyramid.config import Configurator
-from pyramid.view import view_config
-from pyramid.request import Request
-from pyramid.httpexceptions import HTTPFound
-
-from dataclasses import dataclass
-from dataclasses_json import dataclass_json, LetterCase
 import os
+from dataclasses import dataclass
+
 import yaml
+from dataclasses_json import LetterCase, dataclass_json
+from pyramid.config import Configurator
+from pyramid.httpexceptions import HTTPFound
+from pyramid.request import Request
+from pyramid.view import view_config
 
 openapi_spec_path = os.path.join(os.path.dirname(__file__), "openapi.yaml")
 # read base url from openapi.yaml:
@@ -34,6 +34,7 @@
 @dataclass
 class DataHolderBase:
     """Base class for data classes intended to be used as API response bodies"""
+
     def __json__(self, request):
         return self.to_dict()
 
@@ -49,6 +50,7 @@ def includeme(config: Configurator) -> None:
     config.add_route("totp_secret_id", base_url + "/users/{id}/totp-secret")
     config.add_route("rpc_whoami", base_url + "/rpc/whoami")
     config.add_route("user_id", base_url + "/users/{id}")
+    config.add_route("metrics", base_url + "/metrics")
     config.add_route("metadata", base_url + "/metadata")
     config.add_route("metadata_id", base_url + "/metadata/{id}")
     config.add_route("metadatasets", base_url + "/metadatasets")
@@ -64,11 +66,13 @@ def includeme(config: Configurator) -> None:
     config.add_route("rpc_delete_files", base_url + "/rpc/delete-files")
     config.add_route("rpc_delete_metadatasets", base_url + "/rpc/delete-metadatasets")
     config.add_route("rpc_get_file_url", base_url + "/rpc/get-file-url/{id}")
-    config.add_route('register_submit', base_url + "/registrations")
+    config.add_route("register_submit", base_url + "/registrations")
     config.add_route("register_settings", base_url + "/registrationsettings")
     config.add_route("services", base_url + "/services")
     config.add_route("services_id", base_url + "/services/{id}")
-    config.add_route("service_execution", base_url + "/service-execution/{serviceId}/{metadatasetId}")
+    config.add_route(
+        "service_execution", base_url + "/service-execution/{serviceId}/{metadatasetId}"
+    )
 
     # Endpoint outside of openapi
     config.add_route("upload", base_url + "/upload/{id}")
@@ -77,7 +81,7 @@ def includeme(config: Configurator) -> None:
 
 @view_config(
     route_name="api",
-    renderer='json',
+    renderer="json",
     request_method="GET",
 )
 def get(request: Request):

datameta/api/metrics.py

@@ -0,0 +1,59 @@
+# Copyright 2021 Universität Tübingen, DKFZ and EMBL for the German Human Genome-Phenome Archive (GHGA)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import logging
+from dataclasses import dataclass
+
+from pyramid.request import Request
+from pyramid.view import view_config
+
+from ..models import MetaDataSet
+from . import DataHolderBase
+
+log = logging.getLogger(__name__)
+
+
+@dataclass
+class MetricsBase(DataHolderBase):
+    """Base class for Metrics communication to OpenApi"""
+
+    pass
+
+
+@dataclass
+class MetricsResponse(MetricsBase):
+    """MetricsResponse container for OpenApi communication"""
+
+    metadatasets_submitted_count: int
+
+
+@view_config(
+    route_name="metrics",
+    renderer="json",
+    request_method="GET",
+    openapi=True,
+)
+def metrics(request: Request) -> MetricsResponse:
+    """Get metrics of the server."""
+    db = request.dbsession
+
+    query = db.query(MetaDataSet).filter(MetaDataSet.submission_id.isnot(None))
+
+    metadatasets_submitted_count = int(query.count())
+
+    log.info("Server metrics requested.")
+
+    return MetricsResponse(
+        metadatasets_submitted_count=metadatasets_submitted_count,
+    )

datameta/api/openapi.yaml

@@ -15,7 +15,7 @@
 openapi: 3.0.0
 info:
   description: DataMeta
-  version: 1.5.0
+  version: 1.5.1
   title: DataMeta
 
 servers:
@@ -1242,6 +1242,23 @@ paths:
                 $ref: "#/components/schemas/ServerInfoResponse"
         "500":
           description: Internal Server Error
+
+  /metrics:
+    get:
+      summary: Get server metrics
+      description: Get metrics of the DataMeta server serving this API
+      tags:
+        - Server
+      operationId: GetMetrics
+      responses:
+        "200":
+          description: OK
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/MetricsResponse"
+        "500":
+          description: Internal Server Error
 
   /registrations:
     post:
@@ -1895,6 +1912,15 @@ components:
       items:
         $ref: "#/components/schemas/MetaDataResponse"
 
+    MetricsResponse:
+      type: object
+      properties:
+        metadatasetsSubmittedCount:
+          type: integer
+      required:
+        - metadatasetsSubmittedCount
+      additionalProperties: false
+
     ServerInfoResponse:
       type: object
       properties:

setup.py

@@ -67,7 +67,7 @@
 
 setup(
     name                   = 'datameta',
-    version                = '1.1.1',
+    version                = '1.1.2',
     description            = 'DataMeta - submission server for data and associated metadata',
     long_description       = README + '\n\n' + CHANGES,
     author                 = 'Leon Kuchenbecker',

tests/integration/test_metrics.py

@@ -0,0 +1,82 @@
+# Copyright 2021 Universität Tübingen, DKFZ and EMBL for the German Human Genome-Phenome Archive (GHGA)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from datameta.api import base_url
+
+from . import BaseIntegrationTest
+
+FIXTURES_LOAD = [
+    "groups",
+    "users",
+    "apikeys",
+    "services",
+    "metadata",
+    "files_msets",
+    "submissions",
+    "metadatasets",
+    "serviceexecutions",
+]
+
+# Required, with empty dict 401 is returned for a not registered user
+EMPTY_AUTH_HEADER = {"Authorization": f"Bearer {None}"}
+
+
+class TestGetMetricsEmptyServer(BaseIntegrationTest):
+    """Test get metrics with an empty server."""
+
+    def setUp(self):
+        super().setUp()
+
+    def test_metrics(
+        self,
+    ):
+        response = self.testapp.get(
+            url=f"{base_url}/metrics",
+            status=200,
+            headers=EMPTY_AUTH_HEADER,
+        )
+
+        assert response.json["metadatasetsSubmittedCount"] == 0
+
+
+class TestGetMetricsServer(BaseIntegrationTest):
+    """Test get metrics with data."""
+
+    def setUp(self):
+        super().setUp()
+        for fixture in FIXTURES_LOAD:
+            self.fixture_manager.load_fixtureset(fixture)
+        self.fixture_manager.copy_files_to_storage()
+        self.fixture_manager.populate_metadatasets()
+
+    def test_metrics(
+        self,
+    ):
+        # Get submitted metadatasets
+        user = self.fixture_manager.get_fixture("users", "admin")
+        auth_headers = self.apikey_auth(user) if user else {}
+
+        response_metadatasets = self.testapp.get(
+            url=f"{base_url}/metadatasets", headers=auth_headers, status=200
+        )
+
+        response_metrics = self.testapp.get(
+            url=f"{base_url}/metrics",
+            status=200,
+            headers=EMPTY_AUTH_HEADER,
+        )
+
+        assert response_metrics.json["metadatasetsSubmittedCount"] == len(
+            response_metadatasets.json
+        )